› 8iam

Electron Microscopy
3.1Å resolution

Cryo-EM structure of the yeast SPT-ORM2 (ORM2-S3D) complex

Released:
DOI: 10.2210/pdb8iam/pdb
PDB entry 8iam coloured by chain, front view.
PDB entry 8iam coloured by chain, side view.
PDB entry 8iam coloured by chain, top view.
Source organisms:
Primary publication:
Collaborative regulation of yeast SPT-Orm2 complex by phosphorylation and ceramide.
Xie T, Dong F, Han G, Wu X, Liu P, Zhang Z, Zhong J, Niranjanakumari S, Gable K, Gupta SD, Liu W, Harrison PJ, Campopiano DJ, Dunn TM, Gong X
Cell Rep 43 113717 (2024)
PMID: 38285738
Related structures: EMD-35310

Function and Biology Details

Reaction catalysed: 
Palmitoyl-CoA + L-serine = CoA + 3-dehydro-D-sphinganine + CO(2)
Biochemical function:
Biological process:
Cellular component:

Structure analysis Details

Assembly composition:
hetero octamer (preferred)
PDBe Complex ID:
PDB-CPX-239929 (preferred)
Entry contents:
4 distinct polypeptide molecules
Macromolecules (4 distinct):
Long chain base biosynthesis protein 1; Serine palmitoyltransferase 1 Chains: A, E
Molecule details ›
Chains: A, E
Length: 534 amino acids
Theoretical weight: 59.35 KDa
Source organisms: Expression system: Homo sapiens
UniProt:
  • Canonical: Q94IB8 (Residues: 1-81; Coverage: 17%)
  • Canonical: P25045 (Residues: 106-558; Coverage: 81%)
Gene names: AP22, At4g36480, C7A10.880, EMB2779, END8, FBR11, LCB1, TSC2, YMR296C
Sequence domains: Aminotransferase class I and II
Serine palmitoyltransferase 2 Chains: B, F
Molecule details ›
Chains: B, F
Length: 561 amino acids
Theoretical weight: 63.19 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Homo sapiens
UniProt:
  • Canonical: P40970 (Residues: 1-561; Coverage: 100%)
Gene names: D4246, LCB2, SCS1, TSC1, YD9609.16, YDR062W
Sequence domains: Aminotransferase class I and II
Protein ORM2 Chains: D, H
Molecule details ›
Chains: D, H
Length: 216 amino acids
Theoretical weight: 24.96 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Homo sapiens
UniProt:
  • Canonical: Q06144 (Residues: 1-216; Coverage: 100%)
Gene names: ORM2, YLR350W
Sequence domains: ORMDL family
Serine palmitoyltransferase-regulating protein TSC3 Chains: C, G
Molecule details ›
Chains: C, G
Length: 80 amino acids
Theoretical weight: 9.59 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Homo sapiens
UniProt:
  • Canonical: Q3E790 (Residues: 1-80; Coverage: 100%)
Gene names: TSC3, YBR058C-A

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
1 bound ligand:
Ligand Z1T 2 x Z1T
No modified residues

Experiments and Validation Details

Entry percentile scores
Resolution: 3.1Å
Relevant EMDB volumes: EMD-35310
Expression system: Homo sapiens

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